Comparative Genomics of Foot-and-Mouth Disease Virus

TLDR

Viral RNA sequence conservation and genetic diversity influence FMDV infections, host range, and transmission. The study sequenced and comparatively analyzed 103 FMDV isolates, covering all seven serotypes and providing the first complete SAT1 and SAT3 genomes. The genomes revealed highly conserved regions and invariant motifs in UTRs and proteins, with 58 % of amino acids invariant, and uncovered phylogenetic incongruities indicating interserotypic recombination and a novel SAT lineage with distinct nonstructural protein regions.

Abstract

ABSTRACT Here we present complete genome sequences, including a comparative analysis, of 103 isolates of foot-and-mouth disease virus (FMDV) representing all seven serotypes and including the first complete sequences of the SAT1 and SAT3 genomes. The data reveal novel highly conserved genomic regions, indicating functional constraints for variability as well as novel viral genomic motifs with likely biological relevance. Previously undescribed invariant motifs were identified in the 5′ and 3′ untranslated regions (UTR), as was tolerance for insertions/deletions in the 5′ UTR. Fifty-eight percent of the amino acids encoded by FMDV isolates are invariant, suggesting that these residues are critical for virus biology. Novel, conserved sequence motifs with likely functional significance were identified within proteins L pro , 1B, 1D, and 3C. An analysis of the complete FMDV genomes indicated phylogenetic incongruities between different genomic regions which were suggestive of interserotypic recombination. Additionally, a novel SAT virus lineage containing nonstructural protein-encoding regions distinct from other SAT and Euroasiatic lineages was identified. Insights into viral RNA sequence conservation and variability and genetic diversity in nature will likely impact our understanding of FMDV infections, host range, and transmission.